Abstract
Repetitive DNA sequences, satellite DNAs (satDNAs) and transposable elements (TEs) are essential components of the genome landscape, with many different roles in genome function and evolution. Despite significant advances in sequencing technologies and bioinformatics tools, detection and classification of repetitive sequences can still be an obstacle to the analysis of genomic repeats. Here, we summarize how specificities in repetitive DNA organizational patterns can lead to an inability to classify (and study) a significant fraction of bivalve mollusk repetitive sequences. We suggest that the main reasons for this inability are: the predominant association of satDNA arrays with Helitron/Helentron TEs; the existence of many complex loci; and the unusual, highly scattered organization of short satDNA arrays or single monomers across the whole genome. The specificities of bivalve genomes confirm the need for introducing diverse organisms as models in order to understand all aspects of repetitive DNA biology. It is expected that further development of sequencing techniques and synergy among different bioinformatics tools and databases will enable quick and unambiguous characterization and classification of repetitive DNA sequences in assembled genomes.
Highlights
Repetitive DNAs are mainly constituted of satellite DNAs, formed by sequences repeated in tandem, and of mobile elements, interspersed throughout the genome [2]
A substantial number of satellite DNAs (satDNAs) sequences has been found in the form of single, interspersed monomers. They were, in the same manner as arrays of monomers, found either in standalone form, or associated with conserved boxes of Helitron mobile elements, from one or both sides [39]. We believe that this pattern, differing significantly from the classical organizational concept of satDNA, is a significant contributor to the inability to classify a large number of repetitive DNA sequences, especially standalone interspersed monomers
While there are other circumstances that can contribute to the difficulties in the classification of repetitive elements in bivalves, e.g., the existence of species-specific variants of known elements [33], we believe that a significant role is played by: (i) the absence of classical satellite DNAs, (ii) the predominant existence of satDNA arrays of different sizes within the complete and truncated Helitron/Helentron elements, (iii) the existence of combined types of arrays within such elements, (iv) the presence of a large number of single, interspersed monomers throughout the genome and (v) the existence of complex loci generated by insertion, deletion and recombination events in combination with tandemization of repeats and mobile element conserved boxes
Summary
Despite the exponential number of genome sequencing projects arising and spanning all taxa, genomic regions largely composed of repetitive DNA sequences still present substantial technical issues in the assembly of genomes [1]. Repetitive DNAs are mainly constituted of satellite DNAs (satDNAs), formed by sequences repeated in tandem, and of mobile elements, interspersed throughout the genome [2]. According to the established classical view, satDNAs are associated with constitutive heterochromatin which is commonly located at pericentromeric and subtelomeric chromosomal domains and at interstitial loci of the chromosomal arms. They build long arrays of monomers repeated in tandem, comprised of hundreds to thousands of highly similar repeat units [3]. Clear and unambiguous classifications of repetitive fractions of genomes still present a challenge, as described here for bivalve mollusks
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